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World Congress on Engineering 2016, WCE 2016

作者： Gebreyesus, Kidane Desta Chang, Chuan-Hsiung Institute of Information Science Bioinformatics Program Taiwan International Graduate Program Academia Sinica Taipei 115 Taiwan Center for Systems and Synthetic Biology Institute of Biomedical Informatics National Yang-Ming University Taipei 112 Taiwan

ISBN: (纸本)9789881925305

SIR (susceptible, infectious, removed) epidemic models are commonly used in infectious disease study. These models use systems of differential equations to estimate epidemiological parameters. However, differential equations often suffer from numerical challenges. Here, we proposed simple, effective and robust innovative methods for estimating key infectious disease parameters. Our methods are reformed from the SIR models, by adjusting components of model compartments. We illustrated the methods using the recent large disease outbreaks, Ebola virus disease and Middle East respiratory syndrome Coronavirus.

关键词： Coronavirus

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Evolution at the edge of expanding populations

arXiv

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arXiv 2017年

作者： Deforet, Maxime Carmona-Fontaine, Carlos Korolev, Kirill S. Xavier, Joao B. Sorbonne Université Centre National de la Recherche Rcientifique Laboratoire Jean Perrin LJP Paris75005 France Center for Genomics and Systems Biology Department of Biology New York University New York CityNY10003 United States Department of Physics Graduate Program in Bioinformatics Boston University BostonMA02215 Program in Computational Biology Memorial Sloan-Kettering Cancer Center New York CityNY10065 United States

Predicting evolution of expanding populations is critical to control biological threats such as invasive species and cancer metastasis. Expansion is primarily driven by reproduction and dispersal, but nature abounds with examples of evolution where organisms pay a reproductive cost to disperse faster. When does selection favor this 'survival of the fastest?' We searched for a simple rule, motivated by evolution experiments where swarming bacteria evolved into an hyperswarmer mutant which disperses ∼ 100% faster but pays a growth cost of ∼ 10% to make many copies of its flagellum. We analyzed a two-species model based on the Fisher equation to explain this observation: the population expansion rate (v) results from an interplay of growth (r) and dispersal (D) and is independent of the carrying capacity: v = 2 √rD. A mutant can take over the edge only if its expansion rate (v2) exceeds the expansion rate of the established species' (v1);this simple condition (v2> v1) determines the maximum cost in slower growth that a faster mutant can pay and still be able to take over. Numerical simulations and time-course experiments where we tracked evolution by imaging bacteria suggest that our findings are general: less favorable conditions delay but do not entirely prevent the success of the fastest. Thus, the expansion rate defines a traveling wave fitness, which could be combined with trade-offs to predict evolution of expanding populations. Copyright © 2017, The Authors. All rights reserved.

关键词： Bacteria

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A clonal expression biomarker associates with lung cancer mortality (vol 25, pg 1540, 2019)

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NATURE MEDICINE 2020年第7期26卷 1148-1148页

作者： Biswas, Dhruva Birkbak, Nicolai J. Rosenthal, Rachel Hiley, Crispin T. Lim, Emilia L. Papp, Krisztian Boeing, Stefan Krzystanek, Marcin Djureinovic, Dijana La Fleur, Linnea Greco, Maria Doeme, Balazs Fillinger, Janos Brunnstrom, Hans Wu, Yin Moore, David A. Skrzypski, Marcin Abbosh, Christopher Litchfield, Kevin Al Bakir, Maise Watkins, Thomas B. K. Veeriah, Selvaraju Wilson, Gareth A. Jamal-Hanjani, Mariam Moldvay, Judit Botling, Johan Chinnaiyan, Arul M. Micke, Patrick Hackshaw, Allan Bartek, Jiri Csabai, Istvan Szallasi, Zoltan Herrero, Javier McGranahan, Nicholas Swanton, Charles Cancer Research UK Lung Cancer Centre of Excellence University College London Cancer Institute Paul O’Gorman Building London UK Bill Lyons Informatics Centre University College London Cancer Institute Paul O’Gorman Building London UK Cancer Evolution and Genome Instability Laboratory The Francis Crick Institute London UK Department of Molecular Medicine Aarhus University Aarhus Denmark Bioinformatics Research Centre Aarhus University Aarhus Denmark Department of Physics of Complex Systems ELTE Eötvös Loránd University Budapest Hungary Bioinformatics and Biostatistics The Francis Crick Institute London UK Danish Cancer Society Research Center Copenhagen Denmark Department of Immunology Genetics and Pathology Uppsala University Uppsala Sweden Genomics Equipment Park The Francis Crick Institute London UK Department of Tumor Biology National Korányi Institute of Pulmonology Semmelweis University Budapest Hungary Division of Thoracic Surgery Comprehensive Cancer Center Medical University of Vienna Vienna Austria Department of Thoracic Surgery National Institute of Oncology Semmelweis University Budapest Hungary Department of Pathology National Korányi Institute of Pulmonology Semmelweis University Budapest Hungary Department of Pathology National Institute of Oncology Budapest Hungary Lund University Laboratory Medicine Region Skåne Department of Clinical Sciences Lund Pathology Lund Sweden Department of Pathology UCL Cancer Institute London UK Department of Oncology and Radiotherapy Medical University of Gdansk Gdansk Poland SE-NAP Brain Metastasis Research Group 2nd Department of Pathology Semmelweis University Budapest Hungary Michigan Center for Translational Pathology University of Michigan Ann Arbor USA Department of Pathology University of Michigan Ann Arbor USA Rogel Cancer Center University of Michigan Ann Arbor USA Department of Urology University of Michigan Ann Arbor USA Howard Hughes Medical Institute University of Michigan An

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development

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Nature 2020年第7831期586卷 E31页

作者： David U Gorkin Iros Barozzi Yuan Zhao Yanxiao Zhang Hui Huang Ah Young Lee Bin Li Joshua Chiou Andre Wildberg Bo Ding Bo Zhang Mengchi Wang J Seth Strattan Jean M Davidson Yunjiang Qiu Veena Afzal Jennifer A Akiyama Ingrid Plajzer-Frick Catherine S Novak Momoe Kato Tyler H Garvin Quan T Pham Anne N Harrington Brandon J Mannion Elizabeth A Lee Yoko Fukuda-Yuzawa Yupeng He Sebastian Preissl Sora Chee Jee Yun Han Brian A Williams Diane Trout Henry Amrhein Hongbo Yang J Michael Cherry Wei Wang Kyle Gaulton Joseph R Ecker Yin Shen Diane E Dickel Axel Visel Len A Pennacchio Bing Ren Ludwig Institute for Cancer Research La Jolla CA USA. Center for Epigenomics University of California San Diego School of Medicine La Jolla CA USA. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA. Department of Surgery and Cancer Imperial College London London UK. Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA. Biomedical Sciences Graduate Program University of California San Diego School of Medicine La Jolla CA USA. Department of Pediatrics University of California San Diego School of Medicine La Jolla CA USA. Department of Cellular and Molecular Medicine University of California San Diego School of Medicine La Jolla CA USA. Department of Biochemistry and Molecular Biology Penn State School of Medicine Hershey PA USA. Stanford University School of Medicine Department of Genetics Stanford CA USA. Genomic Analysis Laboratory Salk Institute for Biological Studies La Jolla CA USA. Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA. Howard Hughes Medical Institute Salk Institute for Biological Studies La Jolla CA USA. Institute for Human Genetics and University of California San Francisco San Francisco CA USA. Department of Neurology University of California San Francisco San Francisco CA USA. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA. avisel@lbl.gov. US Department of Energy Joint Genome Institute Berkeley CA USA. avisel@lbl.gov. School of Natural Sciences University of California Merced Merced CA USA. avisel@lbl.gov. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA. lapennacchio@lbl.gov. US Department of Energy Joint Genome Institute Berkeley CA USA. lapennacchio@lbl.gov. Comparative Biochemistry Program University of California Berkeley Berkeley CA USA

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Author Correction: FOXA1 repression drives lineage plasticity and immune heterogeneity in bladder cancers with squamous differentiation

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Nature communications 2022年第1期13卷 7920页

作者： Joshua I Warrick Wenhuo Hu Hironobu Yamashita Vonn Walter Lauren Shuman Jenna M Craig Lan L Gellert Mauro A A Castro A Gordon Robertson Fengshen Kuo Irina Ostrovnaya Judy Sarungbam Ying-Bei Chen Anuradha Gopalan Sahussapont J Sirintrapun Samson W Fine Satish K Tickoo Kwanghee Kim Jasmine Thomas Nagar Karan Sizhi Paul Gao Timothy N Clinton Andrew T Lenis Timothy A Chan Ziyu Chen Manisha Rao Travis J Hollman Yanyun Li Nicholas D Socci Shweta Chavan Agnes Viale Neeman Mohibullah Bernard H Bochner Eugene J Pietzak Min Yuen Teo Gopa Iyer Jonathan E Rosenberg Dean F Bajorin Matthew Kaag Suzanne B Merrill Monika Joshi Rosalyn Adam John A Taylor Peter E Clark Jay D Raman Victor E Reuter Yu Chen Samuel A Funt David B Solit David J DeGraff Hikmat A Al-Ahmadie Department of Pathology and Laboratory Medicine Pennsylvania State University College of Medicine Hershey PA USA. Human Oncology and Pathogenesis Program Memorial Sloan Kettering Cancer Center New York NY USA. Department of Urology Pennsylvania State University College of Medicine Hershey PA USA. Department of Public Health Sciences Pennsylvania State University College of Medicine Hershey PA USA. Department of Pathology Microbiology and Immunology Vanderbilt University Medical Center Nashville TN USA. Bioinformatics and Systems Biology Laboratory Federal University of Parana Curitiba Paraná Brazil. BC Cancer Canada's Michael Smith Genome Sciences Centre Vancouver BC Canada. Urology Service Department of Surgery Memorial Sloan Kettering Cancer Center New York NY USA. Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA. Department of Pathology and Laboratory Medicine Memorial Sloan Kettering Cancer Center New York NY USA. Marie-Josée and Henry R. Kravis Center for Molecular Oncology Memorial Sloan Kettering Cancer Center New York NY USA. Department of Medicine Memorial Sloan Kettering Cancer Center New York NY USA. Department of Medicine Division of Hematology-Oncology Penn State Cancer Institute Hershey PA USA. Department of Urology Boston Children's Hospital Boston MA USA. Department of Urology University of Kansas Medical Center Kansas City MO USA. Levine Cancer Institute Atrium Health Charlotte NC USA. Department of Pathology and Laboratory Medicine Pennsylvania State University College of Medicine Hershey PA USA. ddegraff@pennstatehealth.psu.edu. Department of Urology Pennsylvania State University College of Medicine Hershey PA USA. ddegraff@pennstatehealth.psu.edu. Deparment of Biochemistry and Molecular Biology Pennsylvania State University College of Medicine Hershey PA USA. ddegraff@pennstatehealth.psu.edu. Department of Epidemiology and Biostatistics Memorial Sloan Kettering Ca

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Heterogeneity analysis provides evidence for a genetically homogeneous subtype of bipolar-disorder

arXiv

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arXiv 2024年

作者： McGrouther, Caroline C. Rangan, Aaditya V. Florio, Arianna Di Elman, Jeremy A. Schork, Nicholas J. Kelsoe, John Stahl, Eli A. Breen, Gerome Forstner, Andreas J. McQuillin, Andrew Ripke, Stephan Trubetskoy, Vassily Mattheisen, Manuel Wang, Yunpeng Coleman, Jonathan R.I. Gaspar, Héléna A. de Leeuw, Christiaan A. Steinberg, Stacy Whitehead Pavlides, Jennifer M. Trzaskowski, Maciej Byrne, Enda M. Pers, Tune H. Holmans, Peter A. Richards, Alexander L. Abbott, Liam Agerbo, Esben Akil, Huda Albani, Diego Alliey-Rodriguez, Ney Als, Thomas D. Anjorin, Adebayo Antilla, Verneri Awasthi, Swapnil Badner, Judith A. Bækvad-Hansen, Marie Barchas, Jack D. Bass, Nicholas Bauer, Michael Belliveau, Richard Bergen, Sarah E. Pedersen, Carsten Bøcker Bøen, Erlend Boks, Marco P. Boocock, James Budde, Monika Bunney, William Burmeister, Margit Bybjerg-Grauholm, Jonas Byerley, William Casas, Miquel Cerrato, Felecia Cervantes, Pablo Chambert, Kimberly Charney, Alexander W. Chen, Danfeng Churchhouse, Claire Clarke, Toni-Kim Coryell, William Craig, David W. Cruceanu, Cristiana Curtis, David Czerski, Piotr M. Dale, Anders M. de Jong, Simone Degenhardt, Franziska Del-Favero, Jurgen DePaulo, J. Raymond Djurovic, Srdjan Dobbyn, Amanda L. Dumont, Ashley Elvsåshagen, Torbjørn Escott-Price, Valentina Fan, Chun Chieh Fischer, Sascha B. Flickinger, Matthew Foroud, Tatiana M. Forty, Liz Frank, Josef Fraser, Christine Freimer, Nelson B. Frisén, Louise Gade, Katrin Gage, Diane Garnham, Julie Giambartolomei, Claudia Pedersen, Marianne Giørtz Goldstein, Jaqueline Gordon, Scott D. Gordon-Smith, Katherine Green, Elaine K. Green, Melissa J. Greenwood, Tiffany A. Grove, Jakob Guan, Weihua Guzman-Parra, José Hamshere, Marian L. Hautzinger, Martin Heilbronner, Urs Herms, Stefan Hipolito, Maria Hoffmann, Per Holland, Dominic Huckins, Laura Jamain, Stéphane Johnson, Jessica S. Kandaswamy, Radhika Karlsson, Robert Kennedy, James L. Kittel-Schneider, Sarah Knowles, James A. Kogevinas, Manolis Koller, Anna C. Kupka, Ralph Lavebratt, Catharina Lawrence, Jacob Lawson, Courant Institute of Mathematical Sciences New York University New YorkNY United States School of Medicine Division of Psychological Medicine and Clinical Neurosciences Cardiff University Cardiff United Kingdom Department of Psychiatry University of California San Diego San DiegoCA United States The Translational Genomics Research Institute Quantitative Medicine and Systems Biology PhoenixAZ United States Department of Psychiatry University of California San Diego La Jolla CA United States Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New YorkNY United States Department of Psychiatry Icahn School of Medicine at Mount Sinai New YorkNY United States Medical and Population Genetics Broad Institute CambridgeMA United States MRC Social Genetic and Developmental Psychiatry Centre King’s College London London United Kingdom NIHR BRC for Mental Health King’s College London London United Kingdom University of Basel Basel Switzerland Institute of Human Genetics University of Bonn School of Medicine University Hospital Bonn DE Bonn Germany Centre for Human Genetics University of Marburg DE Marburg Germany Institute of Medical Genetics and Pathology University Hospital Basel Basel Switzerland Division of Psychiatry University College London London United Kingdom Stanley Center for Psychiatric Research Broad Institute CambridgeMA United States Department of Psychiatry and Psychotherapy Charité - Universitätsmedizin Berlin Germany Analytic and Translational Genetics Unit Massachusetts General Hospital BostonMA United States iSEQ Center for Integrative Sequencing Aarhus University DK Aarhus Denmark Department of Biomedicine - Human Genetics Aarhus University DK Aarhus Denmark Department of Clinical Neuroscience Centre for Psychiatry Research Karolinska Institutet Stockholm Sweden Department of Psychiatry Psychosomatics and Psychotherapy Center of Mental Health University Hospital Würzburg DE Würzburg Ge

Background: Bipolar Disorder (BD) is a complex disease. It is heterogeneous, both at the phenotypic and genetic level, although the extent and impact of this heterogeneity is not fully understood. One way to assess this heterogeneity is to look for patterns in the subphenotype data. Because of the variability in how phenotypic data was collected by the various BD studies over the years, homogenizing this subphenotypic data is a challenging task, and so is replication. An alternative methodology, taken here, is to set aside the intricacies of subphenotype and allow the genetic data itself to determine which subjects define a homogeneous genetic subgroup (termed ‘bicluster’ below). Results: In this paper, we leverage recent advances in heterogeneity analysis to look for genetically-driven subgroups (i.e., biclusters) within the broad phenotype of Bipolar Disorder. We first apply this covariate-corrected biclustering algorithm to a cohort of 2524 BD cases and 4106 controls from the Bipolar Disease Research Network (BDRN) within the Psychiatric Genomics Consortium (PGC). We find evidence of genetic heterogeneity delineating a statistically significant bicluster comprising a subset of BD cases which exhibits a disease-specific pattern of differential-expression across a subset of SNPs. This disease-specific genetic pattern (i.e., ‘genetic subgroup’) replicates across the remaining data-sets collected by the PGC containing 5781/8289, 3581/7591, and 6825/9752 cases/controls, respectively. This genetic subgroup (discovered without using any BD subtype information) was more prevalent in Bipolar type-I than in Bipolar type-II. Conclusions: Our methodology has successfully identified a replicable homogeneous genetic subgroup of bipolar disorder. This subgroup may represent a collection of correlated genetic risk-factors for BDI. By investigating the subgroup’s bicluster-informed polygenic-risk-scoring (PRS), we find that the disease-specific pattern highlighted by the bicluste

关键词： Economic and social effects

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LifeTime and improving European healthcare through cell-based interceptive medicine (vol 587, pg 377, 2020)

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NATURE 2021年第7852期592卷 E8-E8页

作者： Rajewsky, Nikolaus Almouzni, Genevieve Gorski, Stanislaw A. Aerts, Stein Amit, Ido Bertero, Michela G. Bock, Christoph Bredenoord, Annelien L. Cavalli, Giacomo Chiocca, Susanna Clevers, Hans De Strooper, Bart Eggert, Angelika Ellenberg, Jan Fernandez, Xose M. Figlerowicz, Marek Gasser, Susan M. Hubner, Norbert Kjems, Jorgen Knoblich, Jurgen A. Krabbe, Grietje Lichter, Peter Linnarsson, Sten Marine, Jean-Christophe Marioni, John C. Marti-Renom, Marc A. Netea, Mihai G. Nickel, Dorthe Nollmann, Marcelo Novak, Halina R. Parkinson, Helen Piccolo, Stefano Pinheiro, Ines Pombo, Ana Popp, Christian Reik, Wolf Roman-Roman, Sergio Rosenstiel, Philip Schultze, Joachim L. Stegle, Oliver Tanay, Amos Testa, Giuseppe Thanos, Dimitris Theis, Fabian J. Torres-Padilla, Maria-Elena Valencia, Alfonso Vallot, Celine van Oudenaarden, Alexander Vidal, Marie Voet, Thierry Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany Charité-Universitätsmedizin Berlin Germany Berlin Institute of Health (BIH) Berlin Germany German Center for Cardiovascular Research (DZHK) Partner Site Berlin Berlin Germany Institute for Biology Humboldt University of Berlin Berlin Germany Cardiovascular and Metabolic Sciences Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin Germany Department of Pediatric Oncology/Hematology Charité-Universitätsmedizin Berlin Berlin Germany Institut Curie CNRS PSL Research University Sorbonne Université Nuclear Dynamics Unit Equipe Labellisée Ligue contre le cancer Paris France VIB Center for Brain and Disease Research Leuven Belgium Department of Human Genetics KU Leuven Leuven Belgium Department of Neurosciences KU Leuven Leuven Belgium UK Dementia Research Institute at UCL University College London London UK Wellcome Sanger Institute Wellcome Genome Campus Cambridge UK Department of Immunology Weizmann Institute of Science Rehovot Israel Centre for Genomic Regulation (CRG) Barcelona Institute of Science and Technology Barcelona Spain CNAG-CRG Centre for Genomic Regulation Barcelona Institute of Science and Technology Barcelona Spain Universitat Pompeu Fabra Barcelona Spain ICREA Barcelona Spain CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria Department of Laboratory Medicine Medical University of Vienna Vienna Austria Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases Vienna Austria Department of Medical Humanities Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht The Netherlands Institute of Human Genetics UMR 9002 CNRS and University of Montpellier Montpellier France Department of Experimental Oncology IEO European Institute of Oncology IRCCS Milan Italy Department of Oncology and Hemato

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Pitfalls of restriction enzyme analysis in identifying, characterizing,typing, and naming viral pathogens in the era of whole genome data, as illustrated by HAdV type 55

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Virologica Sinica 2016年第5期31卷 448-453页

作者： Qiwei Zhang Shoaleh Dehghan Donald Seto Biosafety Level-3 Laboratory School of Public HealthSouthern Medical University(Guangdong Provincial Key Laboratory of Tropical Disease Research) Chemistry Department American University Bioinformatics and Computational Biology Program School of Systems BiologyGeorge Mason University

Restriction endonuclease analysis(REA),or restriction fragment length polymorphism(RFLP),was useful for identifying and determining the relatedness and putative identities of microbial strains(Tang et al.,1997)and for... 详细信息

关键词： and naming viral pathogens in the era of whole genome data DLL QS characterizing,typing Pitfalls of restriction enzyme analysis in identifying REA type

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Epigenetic landscapes reveal transcription factors that regulate CD8⁺ T cell differentiation (vol 18, pg 573, 2017)

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NATURE IMMUNOLOGY 2017年第6期18卷 573-582页

作者： Yu, Bingfei Zhang, Kai Milner, J. Justin Toma, Clara Chen, Runqiang Scott-Browne, James P. Pereira, Renata M. Crotty, Shane Chang, John T. Pipkin, Matthew E. Wang, Wei Goldrath, Ananda W. Division of Biological Sciences University of California San Diego La Jolla California USA Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla California USA Division of Vaccine Discovery La Jolla Institute for Allergy and Immunology La Jolla California USA Department of Immunology and Microbial Science The Scripps Research Institute Jupiter Florida USA Division of Signaling and Gene Expression La Jolla Institute for Allergy and Immunology La Jolla California USA Division of Infectious Diseases Department of Medicine University of California San Diego La Jolla California USA Department of Medicine University of California San Diego La Jolla California USA Department of Chemistry and Biochemistry University of California San Diego La Jolla California USA Department of Cellular and Molecular Medicine University of California San Diego La Jolla California USA.

Dynamic changes in the expression of transcription factors (TFs) can influence the specification of distinct CD8+ T cell fates, but the observation of equivalent expression of TFs among differentially fated precursor ... 详细信息

Dynamic changes in the expression of transcription factors (TFs) can influence the specification of distinct CD8⁺ T cell fates, but the observation of equivalent expression of TFs among differentially fated precursor cells suggests additional underlying mechanisms. Here we profiled the genome-wide histone modifications, open chromatin and gene expression of naive, terminal-effector, memory-precursor and memory CD8⁺ T cell populations induced during the in vivo response to bacterial infection. Integration of these data suggested that the expression and binding of TFs contributed to the establishment of subset-specific enhancers during differentiation. We developed a new bioinformatics method using the PageRank algorithm to reveal key TFs that influence the generation of effector and memory populations. The TFs YY1 and Nr3c1, both constitutively expressed during CD8⁺ T cell differentiation, regulated the formation of terminal-effector cell fates and memory-precursor cell fates, respectively. Our data define the epigenetic landscape of differentiation intermediates and facilitate the identification of TFs with previously unappreciated roles in CD8⁺ T cell differentiation.

关键词： Epigenetics in immune cells Immunological memory

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Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses

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npj Genomic Medicine 2024年第1期9卷 49页

作者： Demidov, German Yaldiz, Burcu Garcia-Pelaez, José de Boer, Elke Schuermans, Nika Van de Vondel, Liedewei Paramonov, Ida Johansson, Lennart F. Musacchia, Francesco Benetti, Elisa Bullich, Gemma Sablauskas, Karolis Beltran, Sergi Gilissen, Christian Hoischen, Alexander Ossowski, Stephan de Voer, Richarda Lohmann, Katja Oliveira, Carla Topf, Ana Vissers, Lisenka E. L. M. Zguro, Kristina Zara, Federico Zaganas, Ioannis Yépez, Vicente A. Wirth, Brunhilde Webb, David Verdin, Hannah Van Nieuwenhove, Erika van Montfrans, Joris van Heurck, Roxane van der Veken, Lars Valle, Laura Uva, Paolo Udd, Bjarne Trimouille, Aurelien Thompson, Rachel Tartaglia, Marco Sznajer, Yves Striano, Pasquale Steinke-Lange, Verena Spilioti, Martha Scudieri, Paolo Schröck, Evelin Schon, Katherine Scala, Marcello Savarese, Marco Santen, Gijs W. E. Rump, Andreas Ruivenkamp, Claudia A. L. Roos, Andreas Rooryck, Caroline Riva, Antonella Renieri, Alessandra Ratnaike, Thiloka Radio, Francesca Clementina Privitera, Flavia De la Paz, Manuel Posada Poppe, Bruce Polavarapu, Kiran Platzer, Konrad Peterlin, Borut Pérez-Dueñas, Belén Pauly, Martje Parrini, Elena Olimpio, Catarina Reghan, Mary O. de Benito, Daniel Natera Osorio, Andrés Nascimento Munell, Francina Münchau, Alexander Moortgat, Stéphanie Monestier, Olivier Molnar, Maria Judit Meunier, Colombine Mertes, Christian Mei, Davide Maystadt, Isabelle May, Patrick Maver, Ales Mathioudakis, Lambros Masclaux, Frédéric Mary, Sandrine Delgado, Beatriz Martínez Marcé-Grau, Anna Malaichamy, Sivasankar Macaya, Alfons Luknárová, Rebeka Martín, Estrella López Lochmüller, Hanns Leitão, Elsa Lederer, Damien Leavis, Helen Laner, Andreas Lacombe, Didier Krass, Leon Korff, Christian Kokosali, Evgenia Karakaya, Mert Karadurmus, Deniz Kapaki, Elisabeth Johari, Mridul Iacomino, Michele Huibers, Manon Horvath, Rita Holinski-Feder, Elke Hoffer, Mariette J. V. Herzog, Rebecca Hemelsoet, Dimitri Bouveret, Eva Hammar Haimel, Matthias Hackman, Peter Guerrini, Renzo Grimbacher, Bodo Greally, Marie Ghani, Hamidah Gagneur, Julien Institute of Medical Genetics and Applied Genomics University of Tübingen Tübingen Germany Institute for Bioinformatics and Medical Informatics (IBMI) University of Tübingen Tübingen Germany Department of Human Genetics Radboud University Medical Center Nijmegen Netherlands Department of Clinical Genetics Maastricht University Medical Center Maastricht Netherlands i3S - Instituto de Investigação e Inovação em Saúde Rua Alfredo Allen 208 Porto 4200-135 Portugal IPATIMUP - Institute of Molecular Pathology and Immunology University of Porto Porto Portugal Faculty of Medicine University of Porto Porto Portugal Donders Institute for Brain Cognition and Behaviour Radboud University Nijmegen Netherlands Department of Clinical Genetics Erasmus MC University Medical Center Rotterdam Netherlands Center for Medical Genetics Ghent University Hospital Ghent Belgium Translational Neurosciences Faculty of Medicine and Health Sciences University of Antwerp Antwerp Belgium Laboratory of Neuromuscular Pathology Institute Born-Bunge University of Antwerp Antwerp Belgium Centro Nacional de Análisis Genómico (CNAG) C/Baldiri Reixac 4 Barcelona 08028 Spain Universitat de Barcelona (UB) Barcelona Spain University of Groningen University Medical Center Groningen Department of Genetics Groningen Netherlands Center for Human Technologies Italian Institute of Technology (IIT) Genova Italy Telethon Institute for Genetics and Medicine Pozzuoli (Napoli) 80078 Italy Department of Medical Biotechnologies Med Biotech Hub and Competence Center University of Siena Siena 53100 Italy Institute of Data Science and Digital Technologies Vilnius University Vilnius Lithuania Departament de Genètica Microbiologia i Estadística Facultat de Biologia Universitat de Barcelona (UB) Barcelona Spain Radboud Institute for Molecular Life Sciences Nijmegen Netherlands Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI) Radboud University Medical Center Nijmegen N

We report the results of a comprehensive copy number variant (CNV) reanalysis of 9171 exome sequencing datasets from 5757 families affected by a rare disease (RD). The data reanalysed was extremely heterogeneous, having been generated using 28 different enrichment kits by 42 different research groups across Europe partnering in the Solve-RD project. Each research group had previously undertaken their own analysis of the data but failed to identify disease-causing variants. We applied three CNV calling algorithms to maximise sensitivity, and rare CNVs overlapping genes of interest, provided by four partner European Reference Networks, were taken forward for interpretation by clinical experts. This reanalysis has resulted in a molecular diagnosis being provided to 51 families in this sample, with ClinCNV performing the best of the three algorithms. We also identified partially explanatory pathogenic CNVs in a further 34 individuals. This work illustrates the value of reanalysing ES cold cases for CNVs. © The Author(s) 2024.

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